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- PDB-2kdd: Solution structure of the conserved C-terminal dimerization domai... -

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Basic information

Entry
Database: PDB / ID: 2kdd
TitleSolution structure of the conserved C-terminal dimerization domain of Borealin
ComponentsBorealinCDCA8
KeywordsCELL CYCLE / protein dimer / Cell division / Centromere / Chromosomal protein / Cytoplasm / Mitosis / Nucleus / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / chromosome passenger complex / mitotic metaphase chromosome alignment / intercellular bridge / mitotic sister chromatid segregation ...positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / chromosome passenger complex / mitotic metaphase chromosome alignment / intercellular bridge / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / mitotic cytokinesis / chromosome, centromeric region / mitotic spindle assembly / chromosome organization / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / midbody / nucleolus / protein-containing complex / nucleoplasm / cytosol
Similarity search - Function
Helix Hairpins - #560 / Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLingel, A. / Bourhis, E. / Cochran, A.G. / Fairbrother, W.J.
CitationJournal: Biochemistry / Year: 2009
Title: Phosphorylation of a borealin dimerization domain is required for proper chromosome segregation.
Authors: Bourhis, E. / Lingel, A. / Phung, Q. / Fairbrother, W.J. / Cochran, A.G.
History
DepositionJan 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Borealin
B: Borealin


Theoretical massNumber of molelcules
Total (without water)16,1642
Polymers16,1642
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Borealin / CDCA8 / Dasra-B / hDasra-B / Cell division cycle-associated protein 8 / Pluripotent embryonic stem cell- ...Dasra-B / hDasra-B / Cell division cycle-associated protein 8 / Pluripotent embryonic stem cell-related gene 3 protein


Mass: 8082.155 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species: sapiens / Gene: CDCA8, PESCRG3 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53HL2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1243D 1H-13C NOESY
1323D HNHA
1412D 1H-1H NOESY
1522D 1H-15N HSQC
1653D 1H-13C NOESY
1733D HNCA
1833D HN(CA)CB
1933D CBCA(CO)NH
11033D C(CO)NH
11133D H(CCO)NH
11243D 1H-15N TOCSY
11322D 1H-15N HSQC
11432D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
20.8 mM [U-100% 15N] Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
30.7 mM [U-100% 13C; U-100% 15N] Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
40.7 mM [U-100% 13C; U-100% 15N] Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
50.8 mM 50% [U-100% 13C; U-100% 15N], 50% natural abundance Borealin, 40 mM sodium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMBorealin1
40 mMsodium phosphate1
100 mMsodium chloride1
0.8 mMBorealin[U-100% 15N]2
40 mMsodium phosphate2
100 mMsodium chloride2
0.7 mMBorealin[U-100% 13C; U-100% 15N]3
40 mMsodium phosphate3
100 mMsodium chloride3
0.7 mMBorealin[U-100% 13C; U-100% 15N]4
40 mMsodium phosphate4
100 mMsodium chloride4
0.8 mMBorealin50% [U-100% 13C; U-100% 15N], 50% natural abundance5
40 mMsodium phosphate5
100 mMsodium chloride5
Sample conditionsIonic strength: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 299 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBrukercollection
CCPNCCPNdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
MOLMOLKoradi, Billeter and Wuthrichdisplay
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Distance restraints were derived from 15N- or 13C-resolved 3D NOESY experiments and a 2D homonuclear 1H NOESY experiment. Restraints for the backbone angles phi and psi were derived from ...Details: Distance restraints were derived from 15N- or 13C-resolved 3D NOESY experiments and a 2D homonuclear 1H NOESY experiment. Restraints for the backbone angles phi and psi were derived from TALOS. Stereospecific assignments of Leu, Val methyl groups were obtained using a 10% fractionally 13C-labeled sample. HN-N residual dipolar couplings were measured using a spin-state-selective 1H,15N correlation experiment in dilute liquid crystalline medium.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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